This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. We are modeling the binding of endopolygalacturonase II from Aspergillus niger to polygalacturonic acid (PGA) from cell walls using Amber and Glycam forcefields. In this investigation, there are important amino acid and carbohydrate residues that play a key role in binding, conformational change and catalysis. Employing post-simulational analysis with the MMPBSA approach, we are evaluating substrate binding free energies in solution. We are using surface footprinting by OH radical to identify those regions of the protein surface shielded from oxidation by contact with the substrate By correlating the results with solvent accessible surface areas in the presence and absence of the polygalacturonic acid substrate we will be able to generate a medium resolution model for this complex. Other objectives include investigating the binding of the pectin substrate to enzyme in the presence of the PGIP inhibitor and the effects of the inhibitor on the enzyme/substrate complex.